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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CHCHD4 |
Basic gene info. | Gene symbol | CHCHD4 |
Gene name | coiled-coil-helix-coiled-coil-helix domain containing 4 | |
Synonyms | MIA40|TIMM40 | |
Cytomap | UCSC genome browser: 3p25.1 | |
Genomic location | chr3 :14153576-14166371 | |
Type of gene | protein-coding | |
RefGenes | NM_001098502.1, NM_144636.2, | |
Ensembl id | ENSG00000163528 | |
Description | coiled-coil-helix-coiled-coil-helix domain-containing protein 4mitochondrial intermembrane space import and assembly 40 homologmitochondrial intermembrane space import and assembly protein 40translocase of inner mitochondrial membrane 40 homolog | |
Modification date | 20141207 | |
dbXrefs | MIM : 611077 | |
HGNC : HGNC | ||
Ensembl : ENSG00000163528 | ||
HPRD : 13045 | ||
Vega : OTTHUMG00000129805 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_CHCHD4 | |
BioGPS: 131474 | ||
Gene Expression Atlas: ENSG00000163528 | ||
The Human Protein Atlas: ENSG00000163528 | ||
Pathway | NCI Pathway Interaction Database: CHCHD4 | |
KEGG: CHCHD4 | ||
REACTOME: CHCHD4 | ||
ConsensusPathDB | ||
Pathway Commons: CHCHD4 | ||
Metabolism | MetaCyc: CHCHD4 | |
HUMANCyc: CHCHD4 | ||
Regulation | Ensembl's Regulation: ENSG00000163528 | |
miRBase: chr3 :14,153,576-14,166,371 | ||
TargetScan: NM_001098502 | ||
cisRED: ENSG00000163528 | ||
Context | iHOP: CHCHD4 | |
cancer metabolism search in PubMed: CHCHD4 | ||
UCL Cancer Institute: CHCHD4 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for CHCHD4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: CHCHD4 |
Familial Cancer Database: CHCHD4 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: CHCHD4 |
MedGen: CHCHD4 (Human Medical Genetics with Condition) | |
ClinVar: CHCHD4 | |
Phenotype | MGI: CHCHD4 (International Mouse Phenotyping Consortium) |
PhenomicDB: CHCHD4 |
Mutations for CHCHD4 |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CHCHD4 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
DA459346 | CHCHD4 | 1 | 426 | 3 | 14154470 | 14166256 | BIRC6 | 420 | 575 | 2 | 32664585 | 32664740 | |
BF476043 | CHCHD4 | 13 | 144 | 3 | 14153585 | 14153716 | CAV1 | 135 | 441 | 7 | 116200112 | 116200417 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=6) | (# total SNVs=4) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 10 SNVs Having the Most Samples in COSMIC data |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr3:14154632-14154632 | p.G75S | 2 |
chr3:14154579-14154579 | p.T92T | 1 |
chr3:14154633-14154633 | p.S74S | 1 |
chr3:14157930-14157930 | p.E52E | 1 |
chr3:14157999-14157999 | p.T29T | 1 |
chr3:14154407-14154407 | p.E150* | 1 |
chr3:14163464-14163464 | p.Y5F | 1 |
chr3:14154427-14154427 | p.I143T | 1 |
chr3:14163466-14163466 | p.S4S | 1 |
chr3:14154480-14154480 | p.E125D | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   |   |   | 1 |   |   | 3 |   | 1 |   |   | 2 |   |   |   |   | 2 | 1 |   | 1 |
# mutation |   |   |   | 1 |   |   | 2 |   | 1 |   |   | 2 |   |   |   |   | 2 | 1 |   | 1 |
nonsynonymous SNV |   |   |   | 1 |   |   | 2 |   |   |   |   | 2 |   |   |   |   | 2 | 1 |   |   |
synonymous SNV |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   | 1 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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Top 10 SNVs Having the Most Samples in TCGA data |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr3:14154580 | p.T79M,CHCHD4 | 2 |
chr3:14154632 | p.T79T,CHCHD4 | 1 |
chr3:14154633 | p.G62S,CHCHD4 | 1 |
chr3:14157930 | p.S61R,CHCHD4 | 1 |
chr3:14163467 | p.E39E,CHCHD4 | 1 |
chr3:14154427 | p.S4L | 1 |
chr3:14154485 | p.I130T,CHCHD4 | 1 |
chr3:14154541 | p.D111Y,CHCHD4 | 1 |
chr3:14154566 | p.R92Q,CHCHD4 | 1 |
chr3:14154579 | p.G84R,CHCHD4 | 1 |
Other DBs for Point Mutations |
Copy Number for CHCHD4 in TCGA |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for CHCHD4 |
Gene Expression in Cancer Cell-lines (CCLE) |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
Differential Gene Expression in Primary Tumors (TCGA) |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-Expressed gene's network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
TAMM41,CHCHD4,CMC1,CNOT10,JAGN1,LSM3,MKRN2, MRPS25,MTERF3,NOP16,OXNAD1,OXSM,RAF1,RUVBL1, SGOL1,TCEB1,THUMPD3,TMEM70,TRNT1,TSEN2,UBE2E1 | ADI1,ATP5G3,ATP5H,ATP5J,APOPT1,TIMM21,C22orf39, CHCHD4,CRYAB,EIF2B3,GHITM,GTF3A,HOXA10,HSPB6, LDHA,OPTN,PRKAG1,PSMC2,SETD3,SNAPIN,YBX1 |
ATP5G3,CCDC58,CCNB1,CHCHD4,COQ3,EBNA1BP2,GRPEL1, HSPA9,LSM3,LYAR,MND1,MRPL1,MRPS25,NDUFAF4, NOP16,OXNAD1,OXSM,PDSS1,POC1A,RPUSD3,SFXN4 | ACTL6A,AIMP1,CACYBP,CCDC58,CHCHD4,COMMD10,COPS3, DCAF13,DRG1,EIF2B3,EMG1,MRPL1,MRPL24,MRPL36, MRPL50,MRPS15,TMEM126A,TOMM6,TRIAP1,VDAC3,ZNF576 |
Co-Expressed gene's Protein-protein interaction Network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for CHCHD4 |
There's no related Drug. |
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Cross referenced IDs for CHCHD4 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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